@@ -5,7 +5,7 @@ importMethodsFrom(Biobase, exprs, fData,
55 featureNames, "featureNames<-",
66 pData, "pData<-",
77 sampleNames, "sampleNames<-")
8- import(Biostrings)
8+ import(Biostrings, except = c(type) )
99importMethodsFrom(GenomeInfoDb, seqlevels, "seqlevels<-", genome, "genome<-", seqlengths, "seqlengths<-")
1010importClassesFrom(GenomeInfoDb, Seqinfo)
1111import(GenomicRanges)
@@ -26,7 +26,7 @@ importFrom(beanplot, beanplot)
2626importFrom(nor1mix, norMix, pnorMix, qnorMix)
2727importFrom(siggenes, pi0.est, qvalue.cal)
2828importFrom(limma, squeezeVar, lmFit, eBayes, contrasts.fit, normexp.signal)
29- importFrom(preprocessCore, normalize.quantiles)
29+ importFrom(preprocessCore, normalize.quantiles, normalize.quantiles.use.target )
3030importFrom(illuminaio, readIDAT)
3131importFrom(genefilter, rowFtests, rowttests)
3232importFrom(utils, packageVersion, read.csv, read.table, data)
@@ -44,7 +44,7 @@ importFrom("graphics", "abline", "axis", "legend", "lines", "par",
4444 "plot", "plot.new", "stripchart", "text")
4545importFrom("stats", "approx", "as.formula", "cmdscale", "contrasts",
4646 "dist", "fitted", "kmeans", "lm", "lm.fit", "model.matrix",
47- "pchisq", "pf", "pnorm", " prcomp", "pt", "rnorm", "runif",
47+ "pchisq", "pf", "prcomp", "pt", "rnorm", "runif",
4848 "vcov")
4949
5050export(getManifest, getProbeInfo, getManifestInfo,
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